Producing polished prokaryotic pangenomes with the Panaroo pipeline

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http://hdl.handle.net/10138/318617

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Tonkin-Hill , G , MacAlasdair , N , Ruis , C , Weimann , A , Horesh , G , Lees , J A , Gladstone , R A , Lo , S , Beaudoin , C , Floto , R A , Frost , S D W , Corander , J , Bentley , S D & Parkhill , J 2020 , ' Producing polished prokaryotic pangenomes with the Panaroo pipeline ' , Genome Biology , vol. 21 , no. 1 , 180 . https://doi.org/10.1186/s13059-020-02090-4

Title: Producing polished prokaryotic pangenomes with the Panaroo pipeline
Author: Tonkin-Hill, Gerry; MacAlasdair, Neil; Ruis, Christopher; Weimann, Aaron; Horesh, Gal; Lees, John A.; Gladstone, Rebecca A.; Lo, Stephanie; Beaudoin, Christopher; Floto, R. Andres; Frost, Simon D. W.; Corander, Jukka; Bentley, Stephen D.; Parkhill, Julian
Contributor: University of Helsinki, Helsinki Institute for Information Technology
Date: 2020-07-22
Language: eng
Number of pages: 21
Belongs to series: Genome Biology
ISSN: 1474-760X
URI: http://hdl.handle.net/10138/318617
Abstract: Population-level comparisons of prokaryotic genomes must take into account the substantial differences in gene content resulting from horizontal gene transfer, gene duplication and gene loss. However, the automated annotation of prokaryotic genomes is imperfect, and errors due to fragmented assemblies, contamination, diverse gene families and mis-assemblies accumulate over the population, leading to profound consequences when analysing the set of all genes found in a species. Here, we introduce Panaroo, a graph-based pangenome clustering tool that is able to account for many of the sources of error introduced during the annotation of prokaryotic genome assemblies. Panaroo is available at https://github.com/gtonkinhill/panaroo.
Subject: Bacteria
Pangenome
Prokaryote
Clustering
Horizontal gene transfer
GENES MODEL
GENOME
PROTEIN
ALIGNMENT
ALGORITHM
IDENTIFICATION
GENERATION
FREQUENCY
LIBRARY
1184 Genetics, developmental biology, physiology
111 Mathematics
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